Weight gain/inability to lose is a common hypothyroid symptom. It's very possible that once you get your thyroid levels in control, you won't need the phentermine. Actually, a healthy diet and adequate exercise should take its place, anyway, since most people who take weight loss drugs, regain the weight as soon as they get off the drugs.
Levothyroxine should be taken first thing in the morning on an empty stomach, with a full cup of water.